[Thesis]. Manchester, UK: The University of Manchester; 2016.
Branchial arches (BAs) are a series of transient structures that develop on the ventro-lateral
surface of the head in vertebrate embryos. BAs initially appear as a series of similar
segments; as development proceeds each BA will contribute to different structures.
Here, it was investigated the transcriptional mechanisms that instruct the different
fates of the BAs in development. Initially, each BA contains a blood vessel, known
as aortic arch (AA) artery, that connects the dorsal aorta with the heart. Remodelling
of the AAs is crucial to form the adult heart circulation. This process leads to regression
of the anterior AAs, running though the first and second BAs (BA1 and BA2), and persistence
of the AAs contained in more posterior BAs (PBA). To identify the mechanisms that
control remodelling of the AAs, we compared the transcriptomes and epigenomic landscapes
of different BAs. Using RNA-seq and H3K27Ac ChIP-seq, we uncovered the activation
of a vascular smooth muscle cell (VSMC) differentiation transcriptional program exclusively
in the PBAs (and not in BA1/BA2). In support of this finding, we show that VSMC differentiation
occurs specifically in the PBAs, but not BA1-2 in mouse embryonic development. Despite
the absence of VSMC differentiation in developing BA1-2, cells harvested from these
tissues reveal a spontaneous tendency to differentiate towards VSMC fate when grown
in vitro, and activate several VSMC-specific genes (Myocd, Acta2, Tagln, Jag1). Together,
our results suggest that forming VSMCs is a key process for the persistence of AAs.
We also showed that cells derived from all BAs have the potential to differentiate
to VSMCs in vitro. However, only cells in the PBAs differentiate to VSMCs in vivo,
resulting in the maintenance of posterior AAs. In this study, we also uncovered a
novel transcriptional principle that specifies the fate of BA2. Using ChIP-seq, we
found that binding of Meis transcription factors establish a ground pattern in the
BAs. Hoxa2, which specifies BA2 identity, selects a subset of Meis-bound sites. Meis
binding is strongly increased at these sites, which coincide with active enhancers,
linked to genes highly expressed in the BA2 and regulated by Hoxa2. Thus, Hoxa2 modifies
a ground state binding of Meis to instruct segment-specific transcriptional programs.